Software for automated molecular dynamics studies
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Aug 7, 2026 - Python
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md-simulation
Here are 10 public repositories matching this topic...
lindemann is a python package to calculate the Lindemann index of a lammps trajectory
chemistry analysis cheminformatics simulation molecular-dynamics lammps chemoinformatics gromacs ovito phase-transition lindemann md-simulation phase-transitions lindemann-index transition-phase lammps-trajectory temperature-ramps
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Jun 11, 2024 - Python
A batteries-included toolkit of analysis modules and helper functions for molecular dynamics (MD) simulations.
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May 10, 2024 - Python
Molecular Dynamics From Scratch: a from-zero, educational MD engine built on JAX and OpenMM, with CUDA-12 wheels, pytest validation, and a learning path that walks through forcefields, integrators, and analysis primitives.
python education gpu cuda molecular-dynamics computational-biology openmm computational-chemistry from-scratch jax md-simulation
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Jun 22, 2026 - Python
molecule builder for LAMMPS in Julia
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Dec 18, 2020 - Julia
This repository contains Python scripts to analyze MD & PELE simulations, to preprocess & process the system (pdb files), and many more.
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Apr 2, 2025 - Python
MDSimulator: Python-tkinter GUI for automating GROMACS molecular dynamics simulations — topology generation, solvation, ion addition, energy minimisation, equilibration, and production MD — registered IP (IPO Pakistan, 2023)
python gui bioinformatics simulation molecular-dynamics computational-chemistry tkinter gromacs md-simulation
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May 27, 2026 - Python
GROMOS molecular-dynamics simulations of biomolecular system: force-field parametrization, β-peptide & protein dynamics, liquid properties, alchemical free energies (thermodynamic integration), and NMR/NOE structure refinement, each benchmarked against experiment.
molecular-dynamics computational-chemistry scientific-computing nmr force-field biomolecular-simulation free-energy-calculations computational-biophysics md-simulation gromos thermodynamic-integration protein-simulation
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Jun 5, 2026 - Shell
Calculates change of H bond frequency (stability), average angle and average distance from cpptraj hbond output files and creates a sortable, color coded excel table. The Alignkeys submodule was created by excelforum user shg.
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May 22, 2024
FELBuilder is an automated Python pipeline that automates the complex workflow of Principal Component Analysis (PCA) and Free Energy Landscape (FEL) analysis from Molecular Dynamics (MD) trajectories.
molecular-dynamics computational-biology pca gromacs trajectory-analysis principal-component-analysis md trajectory-clustering fel computational-biophysics md-simulation dimentionality-reduction free-energy-landscape
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Nov 16, 2025 - Python
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